An uptake of zinc (Zn), copper (Cu), and lead (Pb) from aqueous solutions by ion exchange on natural zeolitic tuff has been studied. The Croatian zeolite clinoptilolite from the Donje Jesenje deposit has been used as a natural ion exchanger. The efficiency of removal is higher for Pb and Cu than for Zn ions. Measured concentrations of Si in the liquid phase identify the detachment of the aluminosilicate structure during ion exchange in the presence of H+ and OH− ions. The adsorption isotherm equations; Langmuir–Freundlich, Redlich–Petersen, Toth, Dubinin–Radushkevich, modified Dubinin–Radushkevich, and Lineweawer–Burk were derived from the basic empirical equations, and used for calculation of ion exchange parameters. The best fitting of experimental results to the proposed isotherms was observed in models that assume that ionic species bind first at energetically most favorable sites, with multi-layer adsorption taking place subsequently.